Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states
Abstract Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a qui...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2020-05-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20199167 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849331414909059072 |
|---|---|
| author | Siyu Sun Anastasia Baryshnikova Nathan Brandt David Gresham |
| author_facet | Siyu Sun Anastasia Baryshnikova Nathan Brandt David Gresham |
| author_sort | Siyu Sun |
| collection | DOAJ |
| description | Abstract Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. Here, we studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We performed pooled analysis of genotypes using molecular barcode sequencing (Bar‐seq) to test the role of ~4,000 gene deletion mutants and ~12,000 pairwise interactions between all non‐essential genes and the protein kinase genes TOR1, RIM15, and PHO85 in three different nutrient‐restricted conditions in both proliferative and quiescent cells. We detect up to 10‐fold more genetic interactions in quiescent cells than proliferative cells. We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro‐quiescence signal. The master regulator of quiescence, RIM15, shows distinct genetic interaction profiles in response to different starvation signals. However, vacuole‐related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome‐wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis. |
| format | Article |
| id | doaj-art-c5fb37be5a364fdfbff1e1cbe24f1daf |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2020-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-c5fb37be5a364fdfbff1e1cbe24f1daf2025-08-20T03:46:37ZengSpringer NatureMolecular Systems Biology1744-42922020-05-0116511810.15252/msb.20199167Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular statesSiyu Sun0Anastasia Baryshnikova1Nathan Brandt2David Gresham3Center for Genomics and Systems Biology, New York UniversityCalico Life Science LLCCenter for Genomics and Systems Biology, New York UniversityCenter for Genomics and Systems Biology, New York UniversityAbstract Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. Here, we studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We performed pooled analysis of genotypes using molecular barcode sequencing (Bar‐seq) to test the role of ~4,000 gene deletion mutants and ~12,000 pairwise interactions between all non‐essential genes and the protein kinase genes TOR1, RIM15, and PHO85 in three different nutrient‐restricted conditions in both proliferative and quiescent cells. We detect up to 10‐fold more genetic interactions in quiescent cells than proliferative cells. We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro‐quiescence signal. The master regulator of quiescence, RIM15, shows distinct genetic interaction profiles in response to different starvation signals. However, vacuole‐related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome‐wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis.https://doi.org/10.15252/msb.20199167chronological aginggenetic interactionnutrient starvationquiescencesignaling kinase |
| spellingShingle | Siyu Sun Anastasia Baryshnikova Nathan Brandt David Gresham Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states Molecular Systems Biology chronological aging genetic interaction nutrient starvation quiescence signaling kinase |
| title | Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| title_full | Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| title_fullStr | Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| title_full_unstemmed | Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| title_short | Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| title_sort | genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states |
| topic | chronological aging genetic interaction nutrient starvation quiescence signaling kinase |
| url | https://doi.org/10.15252/msb.20199167 |
| work_keys_str_mv | AT siyusun geneticinteractionprofilesofregulatorykinasesdifferbetweenenvironmentalconditionsandcellularstates AT anastasiabaryshnikova geneticinteractionprofilesofregulatorykinasesdifferbetweenenvironmentalconditionsandcellularstates AT nathanbrandt geneticinteractionprofilesofregulatorykinasesdifferbetweenenvironmentalconditionsandcellularstates AT davidgresham geneticinteractionprofilesofregulatorykinasesdifferbetweenenvironmentalconditionsandcellularstates |